renalware-core 2.0.152 → 2.0.158

data/db/migrate/20201021153832_update_supportive_care_mdm_patients_view.rb

@@ -0,0 +1,7 @@
+class UpdateSupportiveCareMDMPatientsView < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      update_view :supportive_care_mdm_patients, version: 2, revert_to_version: 1
+    end
+  end
+end

data/db/migrate/20201021154809_update_transplant_mdm_patients_view.rb

@@ -0,0 +1,7 @@
+class UpdateTransplantMDMPatientsView < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      update_view :transplant_mdm_patients, version: 2, revert_to_version: 1
+    end
+  end
+end

data/db/migrate/20201023092859_remove_unused_indexes.rb

@@ -0,0 +1,20 @@
+class RemoveUnusedIndexes < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      # Covered by index_admission_requests_on_patient_id_and_deleted_at
+      remove_index(:admission_requests, :patient_id)
+
+      # Covered by index_drug_homecare_forms_on_drug_type_id_and_supplier_id
+      remove_index(:drug_homecare_forms, :drug_type_id)
+
+      # Covered by survey_responses_compound_index (answered_on, patient_id, question_id)
+      remove_index(:survey_responses, :answered_on)
+
+      # Covered by idx_dashboard_component_position (dashboard_id, position)
+      remove_index(:system_dashboard_components, :dashboard_id)
+
+      # Covered by index_letter_mailshot_items_on_mailshot_id_and_letter_id
+      remove_index(:letter_mailshot_items, :mailshot_id)
+    end
+  end
+end

data/db/seeds/default/system/seeds.rb

@@ -3,3 +3,4 @@
 require_relative "./countries"
 require_relative "./roles"
 require_relative "./users"
+require_relative "./view_metadata"

data/db/seeds/default/system/view_metadata.rb

@@ -0,0 +1,91 @@
+# frozen_string_literal: true
+
+module Renalware
+  log "Adding View Metadata" do
+    Renalware::System::ViewMetadata.find_or_create_by!(
+      view_name: "transplant_mdm_patients",
+      scope: "transplant",
+      category: "mdm",
+      schema_name: "renalware"
+    ) do |view|
+      view.slug = "all"
+      view.title = "All"
+      view.position = 1
+      view.filters = [
+        { code: "sex", type: "list" },
+        { code: "tx_status", type: "list" },
+        { code: "on_worryboard", type: "list" },
+        { code: "tx_in_past_3m", type: "list" },
+        { code: "tx_in_past_12m", type: "list" },
+        { code: "patient_name", type: "search" }
+      ]
+      view.columns = [].to_json # empty will display all
+    end
+
+    Renalware::System::ViewMetadata.find_or_create_by!(
+      view_name: "hd_mdm_patients",
+      scope: "hd",
+      category: "mdm",
+      slug: "all",
+      schema_name: "renalware"
+    ) do |view|
+      view.title = "All"
+      view.position = 1
+      view.filters = [
+        { code: :schedule, type: :list },
+        { code: :hospital_unit, type: :list },
+        { code: :named_nurse, type: :list },
+        { code: :on_worryboard, type: :list }
+      ]
+      # schedule: :list,
+      # hospital_unit: :list,
+      # named_nurse: :list,
+      # on_worryboard: :list
+      view.columns = [].to_json # empty will display all
+    end
+
+    Renalware::System::ViewMetadata.find_or_create_by!(
+      view_name: "supportive_care_mdm_patients",
+      scope: "supportive_care",
+      category: "mdm",
+      slug: "all",
+      schema_name: "renalware"
+    ) do |view|
+      view.title = "All"
+      view.position = 1
+      view.filters = [{ code: :on_worryboard, type: :list }].to_json
+      view.columns = [].to_json
+    end
+
+    Renalware::System::ViewMetadata.find_or_create_by!(
+      view_name: "pd_mdm_patients",
+      scope: "pd",
+      category: "mdm",
+      slug: "all",
+      schema_name: "renalware"
+    ) do |view|
+      view.title = "All"
+      view.position = 1
+      view.filters = [{ code: :on_worryboard, type: :list }]
+      view.columns = [].to_json
+    end
+
+    Renalware::System::ViewMetadata.find_or_create_by!(
+      view_name: "low_clearance_mdm_patients",
+      scope: "low_clearance",
+      category: "mdm",
+      slug: "all",
+      schema_name: "renalware"
+    ) do |view|
+      view.title = "All"
+      view.position = 1
+      view.filters = [
+        { code: :on_worryboard, type: :list },
+        { code: :tx_candidate, type: :list },
+        { code: :hgb_range, type: :list },
+        { code: :urea_range, type: :list }
+      ]
+      view.columns = [].to_json
+    end
+  end
+end

data/db/seeds/default/ukrdc/measurement_units.csv

@@ -0,0 +1,12 @@
+"name","description"
+"other","Other"
+"l","Litres"
+"dl","Decilitres"
+"ml","Mililitres"
+"g","Grams"
+"mg","Miligrams"
+"μg","Micrograms"
+"ng","Nanograms"
+"tab","Tablets"
+"units","Units (i.e. for Epoetins)"
+"mmol","Minimols"

data/db/seeds/default/ukrdc/measurement_units.rb

@@ -0,0 +1,15 @@
+# frozen_string_literal: true
+
+module Renalware
+  module UKRDC
+    log "Adding UKRDC measurement units" do
+      file_path = File.join(File.dirname(__FILE__), "measurement_units.csv")
+
+      CSV.foreach(file_path, headers: true) do |row|
+        MeasurementUnit.find_or_create_by!(name: row["name"]) do |mu|
+          mu.description = row["description"]
+        end
+      end
+    end
+  end
+end

data/db/seeds/default/ukrdc/seeds.rb

@@ -1,3 +1,4 @@
 # frozen_string_literal: true
 
 require_relative "./modality_codes"
+require_relative "./measurement_units"

data/db/triggers/update_pathology_observations_nresult_trigger_v01.sql

@@ -0,0 +1,11 @@
+-- Create the trigger which will call out function every time a row in pathology_observations
+-- is inserted or updated
+DROP TRIGGER IF EXISTS update_pathology_observations_nresult_trigger ON pathology_observations;
+CREATE TRIGGER update_pathology_observations_nresult_trigger
+  BEFORE INSERT OR UPDATE
+  ON pathology_observations
+  FOR EACH ROW EXECUTE PROCEDURE update_pathology_observations_nresult_from_trigger();
+
+COMMENT ON TRIGGER update_pathology_observations_nresult_trigger ON pathology_observations IS
+'When a row is updated or inserted into pathology_observations, call a function to try and
+coerce the result into a new float column which can be more easily consumed for graphing etc';

data/db/views/hd_mdm_patients_v01.sql

@@ -0,0 +1,69 @@
+SELECT
+    p.id,
+    p.secure_id,
+    (upper(p.family_name::text) || ', '::text) || p.given_name::text AS patient_name,
+    p.nhs_number,
+    p.local_patient_id AS hospital_numbers,
+    p.sex,
+    p.born_on,
+    rprof.esrf_on,
+    latest_op.performed_on AS last_operation_date,
+    date_part('year'::text, age(p.born_on::timestamp with time zone))::integer AS age,
+    mx.modality_name,
+    case when pw.id > 0 then true else false end as on_worryboard,
+    at.name AS access,
+    ap.started_on AS access_date,
+    aplantype.name AS access_plan,
+    aplan.created_at::date AS plan_date,
+    txrsd.name AS tx_status,
+    unit.name AS hospital_unit,
+    unit.unit_code AS dialysing_at,
+    (named_nurses.family_name::text || ', '::text) || named_nurses.given_name::text AS named_nurse,
+    (((hdp.document -> 'transport'::text) ->> 'has_transport'::text) || ': '::text) || ((hdp.document -> 'transport'::text) ->> 'type'::text) AS transport,
+    (sched.days_text || ' '::text) || upper(diurnal.code::text) AS schedule,
+    (pa."values" -> 'HGB'::text) ->> 'result'::text AS hgb,
+    ((pa."values" -> 'HGB'::text) ->> 'observed_at'::text)::date AS hgb_date,
+    (pa."values" -> 'PHOS'::text) ->> 'result'::text AS phos,
+    ((pa."values" -> 'PHOS'::text) ->> 'observed_at'::text)::date AS phos_date,
+    (pa."values" -> 'POT'::text) ->> 'result'::text AS pot,
+    ((pa."values" -> 'POT'::text) ->> 'observed_at'::text)::date AS pot_date,
+    (pa."values" -> 'PTHI'::text) ->> 'result'::text AS pthi,
+    ((pa."values" -> 'PTHI'::text) ->> 'observed_at'::text)::date AS pthi_date,
+    (pa."values" -> 'URR'::text) ->> 'result'::text AS urr,
+    ((pa."values" -> 'URR'::text) ->> 'observed_at'::text)::date AS urr_date
+   FROM patients p
+     JOIN patient_current_modalities mx ON mx.patient_id = p.id AND mx.modality_code::text = 'hd'::text
+     LEFT JOIN hd_profiles hdp ON hdp.patient_id = p.id AND hdp.deactivated_at IS NULL
+     LEFT JOIN hospital_units unit ON unit.id = hdp.hospital_unit_id
+     LEFT JOIN users named_nurses ON named_nurses.id = hdp.named_nurse_id
+     left join patient_worries pw on pw.patient_id  = p.id
+     LEFT JOIN hd_schedule_definitions sched ON sched.id = hdp.schedule_definition_id
+     LEFT JOIN hd_diurnal_period_codes diurnal ON diurnal.id = sched.diurnal_period_id
+     LEFT JOIN pathology_current_observation_sets pa ON pa.patient_id = p.id
+     LEFT JOIN ( SELECT DISTINCT ON (access_profiles.patient_id) access_profiles.id,
+            access_profiles.patient_id,
+            access_profiles.formed_on,
+            access_profiles.started_on,
+            access_profiles.terminated_on,
+            access_profiles.type_id,
+            access_profiles.side,
+            access_profiles.notes,
+            access_profiles.created_by_id,
+            access_profiles.updated_by_id,
+            access_profiles.created_at,
+            access_profiles.updated_at,
+            access_profiles.decided_by_id
+           FROM access_profiles
+          WHERE access_profiles.terminated_on IS NULL
+          ORDER BY access_profiles.patient_id, access_profiles.created_at DESC) ap ON ap.patient_id = p.id
+     LEFT JOIN access_types at ON at.id = ap.type_id
+     LEFT JOIN access_plans aplan ON aplan.patient_id = p.id AND aplan.terminated_at IS NULL
+     LEFT JOIN access_plan_types aplantype ON aplantype.id = aplan.plan_type_id
+     LEFT JOIN transplant_registrations txr ON txr.patient_id = p.id
+     LEFT JOIN transplant_registration_statuses txrs ON txrs.registration_id = txr.id AND txrs.terminated_on IS NULL
+     LEFT JOIN transplant_registration_status_descriptions txrsd ON txrsd.id = txrs.description_id
+     LEFT JOIN renal_profiles rprof ON rprof.patient_id = p.id
+     LEFT JOIN ( SELECT DISTINCT ON (transplant_recipient_operations.patient_id) transplant_recipient_operations.patient_id,
+            transplant_recipient_operations.performed_on
+           FROM transplant_recipient_operations
+          ORDER BY transplant_recipient_operations.patient_id, transplant_recipient_operations.performed_on DESC) latest_op ON latest_op.patient_id = p.id;

data/db/views/hd_mdm_patients_v02.sql

@@ -0,0 +1,70 @@
+SELECT
+    p.id,
+    p.secure_id,
+    (upper(p.family_name::text) || ', '::text) || p.given_name::text AS patient_name,
+    p.nhs_number,
+    p.local_patient_id AS hospital_numbers,
+    p.sex,
+    p.born_on,
+    rprof.esrf_on,
+    latest_op.performed_on AS last_operation_date,
+    date_part('year'::text, age(p.born_on::timestamp with time zone))::integer AS age,
+    mx.modality_name,
+    case when pw.id > 0 then true else false end as on_worryboard,
+    at.name AS access,
+    (select bmi from clinic_visits cv2 where cv2.patient_id = P.id and bmi > 0 order by date desc limit 1) as bmi,
+    ap.started_on AS access_date,
+    aplantype.name AS access_plan,
+    aplan.created_at::date AS plan_date,
+    txrsd.name AS tx_status,
+    unit.name AS hospital_unit,
+    unit.unit_code AS dialysing_at,
+    (named_nurses.family_name::text || ', '::text) || named_nurses.given_name::text AS named_nurse,
+    (((hdp.document -> 'transport'::text) ->> 'has_transport'::text) || ': '::text) || ((hdp.document -> 'transport'::text) ->> 'type'::text) AS transport,
+    (sched.days_text || ' '::text) || upper(diurnal.code::text) AS schedule,
+    (pa."values" -> 'HGB'::text) ->> 'result'::text AS hgb,
+    ((pa."values" -> 'HGB'::text) ->> 'observed_at'::text)::date AS hgb_date,
+    (pa."values" -> 'PHOS'::text) ->> 'result'::text AS phos,
+    ((pa."values" -> 'PHOS'::text) ->> 'observed_at'::text)::date AS phos_date,
+    (pa."values" -> 'POT'::text) ->> 'result'::text AS pot,
+    ((pa."values" -> 'POT'::text) ->> 'observed_at'::text)::date AS pot_date,
+    (pa."values" -> 'PTHI'::text) ->> 'result'::text AS pthi,
+    ((pa."values" -> 'PTHI'::text) ->> 'observed_at'::text)::date AS pthi_date,
+    (pa."values" -> 'URR'::text) ->> 'result'::text AS urr,
+    ((pa."values" -> 'URR'::text) ->> 'observed_at'::text)::date AS urr_date
+   FROM patients p
+     JOIN patient_current_modalities mx ON mx.patient_id = p.id AND mx.modality_code::text = 'hd'::text
+     LEFT JOIN hd_profiles hdp ON hdp.patient_id = p.id AND hdp.deactivated_at IS NULL
+     LEFT JOIN hospital_units unit ON unit.id = hdp.hospital_unit_id
+     LEFT JOIN users named_nurses ON named_nurses.id = hdp.named_nurse_id
+     left join patient_worries pw on pw.patient_id  = p.id
+     LEFT JOIN hd_schedule_definitions sched ON sched.id = hdp.schedule_definition_id
+     LEFT JOIN hd_diurnal_period_codes diurnal ON diurnal.id = sched.diurnal_period_id
+     LEFT JOIN pathology_current_observation_sets pa ON pa.patient_id = p.id
+     LEFT JOIN ( SELECT DISTINCT ON (access_profiles.patient_id) access_profiles.id,
+            access_profiles.patient_id,
+            access_profiles.formed_on,
+            access_profiles.started_on,
+            access_profiles.terminated_on,
+            access_profiles.type_id,
+            access_profiles.side,
+            access_profiles.notes,
+            access_profiles.created_by_id,
+            access_profiles.updated_by_id,
+            access_profiles.created_at,
+            access_profiles.updated_at,
+            access_profiles.decided_by_id
+           FROM access_profiles
+          WHERE access_profiles.terminated_on IS NULL
+          ORDER BY access_profiles.patient_id, access_profiles.created_at DESC) ap ON ap.patient_id = p.id
+     LEFT JOIN access_types at ON at.id = ap.type_id
+     LEFT JOIN access_plans aplan ON aplan.patient_id = p.id AND aplan.terminated_at IS NULL
+     LEFT JOIN access_plan_types aplantype ON aplantype.id = aplan.plan_type_id
+     LEFT JOIN transplant_registrations txr ON txr.patient_id = p.id
+     LEFT JOIN transplant_registration_statuses txrs ON txrs.registration_id = txr.id AND txrs.terminated_on IS NULL
+     LEFT JOIN transplant_registration_status_descriptions txrsd ON txrsd.id = txrs.description_id
+     LEFT JOIN renal_profiles rprof ON rprof.patient_id = p.id
+     LEFT JOIN ( SELECT DISTINCT ON (transplant_recipient_operations.patient_id) transplant_recipient_operations.patient_id,
+            transplant_recipient_operations.performed_on
+           FROM transplant_recipient_operations
+          ORDER BY transplant_recipient_operations.patient_id, transplant_recipient_operations.performed_on DESC) latest_op ON latest_op.patient_id = p.id;

data/db/views/low_clearance_mdm_patients_v01.sql

@@ -0,0 +1,38 @@
+select
+  P.id,
+  P.secure_id,
+  (upper(P.family_name) || ', ' || P.given_name) as "patient_name",
+  P.nhs_number,
+  P.local_patient_id as hospital_numbers,
+  P.sex,
+  P.born_on,
+  date_part('year', age(P.born_on)) as "age",
+  RPROF.esrf_on,
+  Mx.modality_name,
+  case when pw.id > 0 then true else false end as on_worryboard,
+  TXRSD."name" tx_status,
+  PA.values -> 'HGB' ->> 'result' as hgb,
+  (PA.values -> 'HGB' ->> 'observed_at')::date as hgb_date,
+  PA.values -> 'URE' ->> 'result' as ure,
+  (PA.values -> 'URE' ->> 'observed_at')::date as ure_date,
+  PA.values -> 'CRE' ->> 'result' as cre,
+  (PA.values -> 'CRE' ->> 'observed_at')::date as cre_date,
+  PA.values -> 'EGFR' ->> 'result' as egfr,
+  case when TXRSD.code not ilike '%permanent' then true else false end as tx_candidate,
+  case
+    when (convert_to_float(PA.values->'HGB'->>'result') < 100.0) then '< 100'
+    when (convert_to_float(PA.values->'HGB'->>'result') > 130.0) then '> 130'
+    else NULL
+  end as hgb_range,
+  case
+    when (convert_to_float(values->'URE'->>'result') >= 30.0) then '>= 30'
+    else NULL
+  end as urea_range
+from renalware.patients P
+left join patient_worries pw on pw.patient_id = p.id
+left outer join renalware.pathology_current_observation_sets PA on PA.patient_id = P.id
+left outer join renalware.renal_profiles RPROF on RPROF.patient_id = P.id
+left outer join renalware.transplant_registrations TXR on TXR.patient_id = P.id
+left outer join renalware.transplant_registration_statuses TXRS on TXRS.registration_id = TXR.id AND TXRS.terminated_on IS null and TXRS.started_on <= current_date
+left outer join renalware.transplant_registration_status_descriptions TXRSD on TXRSD.id = TXRS.description_id
+inner join renalware.patient_current_modalities Mx on Mx.patient_id = P.id and Mx.modality_code = 'low_clearance'

data/db/views/low_clearance_mdm_patients_v02.sql

@@ -0,0 +1,39 @@
+select
+  P.id,
+  P.secure_id,
+  (upper(P.family_name) || ', ' || P.given_name) as "patient_name",
+  P.nhs_number,
+  P.local_patient_id as hospital_numbers,
+  P.sex,
+  P.born_on,
+  date_part('year', age(P.born_on)) as "age",
+  RPROF.esrf_on,
+  Mx.modality_name,
+  case when pw.id > 0 then true else false end as on_worryboard,
+  (select bmi from clinic_visits where patient_id = P.id and bmi > 0 order by date desc limit 1) as bmi,
+  TXRSD."name" tx_status,
+  PA.values -> 'HGB' ->> 'result' as hgb,
+  (PA.values -> 'HGB' ->> 'observed_at')::date as hgb_date,
+  PA.values -> 'URE' ->> 'result' as ure,
+  (PA.values -> 'URE' ->> 'observed_at')::date as ure_date,
+  PA.values -> 'CRE' ->> 'result' as cre,
+  (PA.values -> 'CRE' ->> 'observed_at')::date as cre_date,
+  PA.values -> 'EGFR' ->> 'result' as egfr,
+  case when TXRSD.code not ilike '%permanent' then true else false end as tx_candidate,
+  case
+    when (convert_to_float(PA.values->'HGB'->>'result') < 100.0) then '< 100'
+    when (convert_to_float(PA.values->'HGB'->>'result') > 130.0) then '> 130'
+    else NULL
+  end as hgb_range,
+  case
+    when (convert_to_float(values->'URE'->>'result') >= 30.0) then '>= 30'
+    else NULL
+  end as urea_range
+from renalware.patients P
+left join patient_worries pw on pw.patient_id = p.id
+left outer join renalware.pathology_current_observation_sets PA on PA.patient_id = P.id
+left outer join renalware.renal_profiles RPROF on RPROF.patient_id = P.id
+left outer join renalware.transplant_registrations TXR on TXR.patient_id = P.id
+left outer join renalware.transplant_registration_statuses TXRS on TXRS.registration_id = TXR.id AND TXRS.terminated_on IS null and TXRS.started_on <= current_date
+left outer join renalware.transplant_registration_status_descriptions TXRSD on TXRSD.id = TXRS.description_id
+inner join renalware.patient_current_modalities Mx on Mx.patient_id = P.id and Mx.modality_code = 'low_clearance'

data/db/views/patient_current_modalities_v02.sql

@@ -0,0 +1,18 @@
+select
+  patients.id as patient_id,
+  patients.secure_id as patient_secure_id,
+  current_modality.id as modality_id,
+  modality_descriptions.id as modality_description_id,
+  modality_descriptions.name as modality_name,
+  current_modality.started_on as started_on,
+  modality_descriptions.code as modality_code
+from patients
+  -- this join only required as currently there can be > 1 current modality for a patient
+  -- here we select the current modality with the most recent started_on
+  left outer join (
+    select distinct on (patient_id) * from modality_modalities
+    where ended_on is null
+    order by patient_id, started_on desc, created_at desc
+) as current_modality
+on patients.id = current_modality.patient_id
+left outer join modality_descriptions on modality_descriptions.id = current_modality.description_id;

data/db/views/pd_mdm_patients_v01.sql

@@ -0,0 +1,42 @@
+select
+  distinct on (P.id)
+  P.id,
+  P.secure_id,
+  (upper(P.family_name) || ', ' || P.given_name) as "patient_name",
+  P.nhs_number,
+  P.local_patient_id as hospital_numbers,
+  P.sex,
+  P.born_on,
+  date_part('year', age(P.born_on)) as "age",
+  RPROF.esrf_on,
+  Mx.modality_name,
+  case
+    when pw.id > 0 then true
+    else false
+    end as on_worryboard,
+  TXRSD."name" tx_status,
+  case pr.type
+    when 'Renalware::PD::APDRegime' then 'APD'
+    when 'Renalware::PD::CAPDRegime' then 'CAPD'
+    end as pd_type,
+  pesi.diagnosis_date as last_esi_date,
+  ppe.diagnosis_date as last_peritonitis_date,
+  PA.values -> 'HGB' ->> 'result' as hgb,
+  (PA.values -> 'HGB' ->> 'observed_at')::date as hgb_date,
+  PA.values -> 'URE' ->> 'result' as ure,
+  (PA.values -> 'URE' ->> 'observed_at')::date as ure_date,
+  PA.values -> 'CRE' ->> 'result' as cre,
+  (PA.values -> 'CRE' ->> 'observed_at')::date as cre_date,
+  PA.values -> 'EGFR' ->> 'result' as egfr
+from renalware.patients P
+left join patient_worries pw on pw.patient_id  = p.id
+left outer join renalware.pathology_current_observation_sets PA on PA.patient_id = P.id
+left outer join renalware.renal_profiles RPROF on RPROF.patient_id = P.id
+left outer join renalware.transplant_registrations TXR on TXR.patient_id = P.id
+left outer join renalware.transplant_registration_statuses TXRS on TXRS.registration_id = TXR.id AND TXRS.terminated_on IS NULL
+left outer join renalware.transplant_registration_status_descriptions TXRSD on TXRSD.id = TXRS.description_id
+left outer join renalware.pd_regimes pr on pr.patient_id = P.id and pr.start_date <= current_date and pr.end_date is null
+left outer join renalware.pd_exit_site_infections pesi on pesi.patient_id = P.id
+left outer join pd_peritonitis_episodes ppe on ppe.patient_id = P.id
+inner join renalware.patient_current_modalities Mx on Mx.patient_id = P.id and Mx.modality_code = 'pd'
+order by P.id, pr.start_date desc, pr.created_at desc, pesi.diagnosis_date desc, ppe.diagnosis_date desc;